rs10878983

Variant names:

• chr12-69432313-G-A
• rs10878983
• ENST00000776073.1:n.372+8186G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000776073.1(LINC02373):​n.372+8186G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.447 in 151,746 control chromosomes in the GnomAD database, including 15,408 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.45 (15408 hom., cov: 30)
• Consequence: LINC02373 ENST00000776073.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.122
• Publications: 4 publications found

Genes affected

LINC02373 (HGNC:53295): (long intergenic non-protein coding RNA 2373)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.499 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02373	ENST00000776073.1	n.372+8186G>A		intron_variant	Intron 3 of 4
LINC02373	ENST00000776074.1	n.176+600G>A		intron_variant	Intron 1 of 3
LINC02373	ENST00000776075.1	n.155+600G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67792 AN: 151628 Hom.: 15388 Cov.: 30

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.463

Gnomad EAS AF: 0.442

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.479

Gnomad OTH AF: 0.457

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.447 AC: 67852 AN: 151746 Hom.: 15408 Cov.: 30 AF XY: 0.445 AC XY: 32996 AN XY: 74128

African (AFR) AF: 0.375 AC: 15501 AN: 41360

American (AMR) AF: 0.508 AC: 7747 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.463 AC: 1604 AN: 3468

East Asian (EAS) AF: 0.442 AC: 2275 AN: 5144

South Asian (SAS) AF: 0.436 AC: 2098 AN: 4810

European-Finnish (FIN) AF: 0.441 AC: 4638 AN: 10522

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.479 AC: 32535 AN: 67892

Other (OTH) AF: 0.454 AC: 956 AN: 2108

Alfa AF: 0.475 Hom.: 33100

Bravo AF: 0.447

Asia WGS AF: 0.417 AC: 1449 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.2
DANN	Benign	0.41
PhyloP100		0.12

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10878983; hg19: chr12-69826093;